[AndrewC]

I'm failing to understand how a sequence with four differences is closer than an identical sequence.

When one is over a range of 263 and the other is over a range of 194.

[Right Wing Professor]

Andrew, a sequence of 263 amino acids is one termination or initiation codon different from a sequence of 194. I know very little about S4, but I'm willing to bet the extra amino acids, in species where they're present, are deleted in post-translation processing.